Sequence
atgc intronic sequence ATGC exonic sequence...tgatcatcatttttcatatgcaagagtatcttcatctatctaattttgtcatttgcggtaaaggttctaatgcgaaaatttgatgtgtgttatatcttagGTCATAGCTCTTCGGGGGTCTTACCATGGAGATACTTTAGGAGCAATGGAAGCACAAGCACCATCACCTTATACAGGCTTTCTCCAGCAGCCGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57590.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 6
tgatcatcatttttcatatgcaagagtatcttcatct-atctaattttgtcatttgc-ggtaaaggttctaatgcgaa--aatttgatgt---gtgttatatcttagGTCATAGCTCTTCGGGGGTCTTACCATGGAGATACTTTAGGAGCAATGGAAGCACAAGCACCATCACCTTATACAGGCTTTCTCCAGCAGCCGTG
|| || | | | | | || || ||||| || | ||| | | ||| | | | || | |||||| | |||| | | |||||||||||||| || || || ||||| ||||||||||| || ||||||||||| || |||||| | ||||| || ||||| || || || ||
-------gggttatcgaaagtgaaatttactcaattagatctagttaggcatgctgctaattcatgttgaactactaatcattttgatattctgtgtcttcattcagGTCATAGCTCTTAAAGGATCATATCATGGTGATACTTTAGGCGCTATGGAAGCACAGGCGCCATCATCGTATACGGGATTTCTTCAACAACCATG
upper sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ22227 (Selaginella moellendorffii), 3'ss of exon 6
tgatcatcatttttcatatgcaagagtatcttcatctatctaattttgtcatttgcggtaaaggttctaatgcgaaaatttgatgtgtgttatatcttagGTCATAGCTCTTCGGGGGTCTTACCATGGAGATACTTTAGGAGCAATGGAAGCACAAGCACCATCACCTTATACAGGCTTTCTCCAGCAGCCGTG
|| | | || | || | || |||| | ||| | || |||| | || || | || || || |||||||| ||||| |||||||||||||| ||||| ||||| ||||| ||||| ||| ||||| || ||
-----------------------------------------------gtaagctttcgttgtgtttatcat-------tttgccgattgtgctg-ctcagGTTCTTGCACTCAGAGGCTCCTATCATGGAGACACTTTGGGAGCAATGGAAGCGCAAGCGCCATCTCCTTACACAGGATTTTCGCAGCAACCTTG
upper sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ25518 (Selaginella moellendorffii), 3'ss of exon 6
tgatcatcatttttcatatgcaagagtatcttcatctatctaattttgtcatttgcggtaaaggttc-taatgcgaa--aatttgatgtgtgttatatcttagGTCATAGCTCTTCGGGGGTCTTACCATGGAGATACTTTAGGAGCAATGGAAGCACAAGCACCATCACCTTATACAGGCTTTCTCCAGCAGCCGTG
|| || | | ||||| ||| | || | | |||| | ||| | || |||| | || || | || || || |||||||| ||||| |||||||||||||| ||||| ||||| ||||| ||||| ||| ||||| || ||
-----------------------------------------------gtaatcttctctaaagtttcgttgtgtttatcattttgccgattgtgctg-ctcagGTTCTTGCACTCAGAGGCTCCTATCATGGAGACACTTTGGGAGCAATGGAAGCGCAAGCGCCATCTCCTTACACAGGATTTTCGCAGCAACCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtcatttgcggtaaaggttctaatgcgaaaatttgatgtgtgttatatcttagGTCATAGCTCTTCGGGGGTCTTACCATGGAGATACTTTAGGAGCAATGGAAGCACAAGCACCATCACCTTATACAGGCTTTCTCCAGCAGCCGTG
aaaatttgat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatcatcatttttcatatgcaagagtatcttcatctatctaattttgtcatttgcggtaaaggttctaatgcgaaaatttgatgtgtgttatatcttagGTCATAGCTCTTCGGGGGTCTTACCATGGAGATACTTTAGGAGCAATGGAAGCACAAGCACCATCACCTTATACAGGCTTTCTCCAGCAGCCGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcgaaaa